[English] 日本語
Yorodumi
- PDB-7yxb: MHC-II dynamics are maintained in HLA-DR allotypes to ensure cata... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yxb
TitleMHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange
Components
  • (HLA class II histocompatibility ...) x 2
  • CLIP peptide
KeywordsIMMUNE SYSTEM / HLA-DR4 / CLIP peptide / MHCII
Function / homology
Function and homology information


myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane ...myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / immunological synapse / PD-1 signaling / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / early endosome membrane / adaptive immune response / lysosome / endosome membrane / immune response / lysosomal membrane / Golgi membrane / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
CITRATE ANION / HLA class II histocompatibility antigen DR beta chain / HLA class II histocompatibility antigen, DR alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.095 Å
AuthorsRoske, Y. / Abualrous, E.T. / Freund, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange.
Authors: Abualrous, E.T. / Stolzenberg, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Gunther, M. / Dahn, S. / Boesen, B.B. / Calvo, M.M. / Biese, C. / Kuppler, F. / Medina-Garcia, A. / Alvaro- ...Authors: Abualrous, E.T. / Stolzenberg, S. / Sticht, J. / Wieczorek, M. / Roske, Y. / Gunther, M. / Dahn, S. / Boesen, B.B. / Calvo, M.M. / Biese, C. / Kuppler, F. / Medina-Garcia, A. / Alvaro-Benito, M. / Hofer, T. / Noe, F. / Freund, C.
History
DepositionFeb 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen DR beta chain
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen DR beta chain
G: CLIP peptide
H: CLIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,44624
Polymers95,0756
Non-polymers1,37118
Water10,989610
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen DR beta chain
G: CLIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,28513
Polymers47,5373
Non-polymers74810
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-20 kcal/mol
Surface area18530 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen DR beta chain
H: CLIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,16111
Polymers47,5373
Non-polymers6248
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-22 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.891, 111.485, 212.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
HLA class II histocompatibility ... , 2 types, 4 molecules ACBD

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 22207.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Plasmid: pFastBacDual-Sf9 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen DR beta chain / MHC class II antigen


Mass: 23193.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pFastBacDual-Sf9 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A1V1IGJ9

-
Protein/peptide , 1 types, 2 molecules GH

#3: Protein/peptide CLIP peptide


Mass: 2136.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFastBacDual-Sf9 / Production host: Baculovirus expression vector pFastBac1-HM

-
Non-polymers , 3 types, 628 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Ammoniumcitrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.09→44.081 Å / Num. obs: 67120 / % possible obs: 99 % / Redundancy: 4.56 % / Biso Wilson estimate: 36.44 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.0159 / Net I/σ(I): 9.69
Reflection shellResolution: 2.09→2.22 Å / Mean I/σ(I) obs: 1.28 / Num. unique obs: 10573 / CC1/2: 0.491 / Rrim(I) all: 0.151

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X5X

4x5x


Resolution: 2.095→44.081 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2221 2099 3.13 %
Rwork0.187 64979 -
obs0.1881 67078 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.91 Å2 / Biso mean: 49.4868 Å2 / Biso min: 19.37 Å2
Refinement stepCycle: final / Resolution: 2.095→44.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6418 0 90 610 7118
Biso mean--72.45 52 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056690
X-RAY DIFFRACTIONf_angle_d0.7419070
X-RAY DIFFRACTIONf_chiral_restr0.05958
X-RAY DIFFRACTIONf_plane_restr0.0051184
X-RAY DIFFRACTIONf_dihedral_angle_d8.5034300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0951-2.14380.33031330.3047414296
2.1438-2.19740.36471390.2931426698
2.1974-2.25680.28841370.2679429499
2.2568-2.32320.26141400.259431099
2.3232-2.39820.2991390.26524313100
2.3982-2.48390.28941400.2442433499
2.4839-2.58340.28031380.2342427599
2.5834-2.70090.25521390.2213429299
2.7009-2.84330.25641410.2095437699
2.8433-3.02140.27931400.19824330100
3.0214-3.25460.20481410.1861435599
3.2546-3.5820.20441410.17314373100
3.582-4.10.18431420.1499438699
4.1-5.16430.14361430.12444425100
5.1643-44.080.22441460.1755450898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.44970.37420.44930.65890.02650.6471-0.01510.1017-0.25910.00550.0631-0.07450.08450.0439-0.060.237-0.01210.03460.1572-0.00830.272324.832214.9817-11.7425
21.80620.88510.15140.93170.00050.7088-0.05830.10370.1718-0.08580.04970.0525-0.0810.03910.00910.21110.01690.01650.14090.030.246317.310629.8071-13.9456
32.3751.63981.32111.69340.41561.8983-0.11220.610.0971-0.15040.16860.0201-0.30870.0761-0.05830.40720.04370.03470.5687-0.01980.232628.943932.2935-39.0667
43.13960.53750.92430.2155-0.49711.8426-0.01750.6504-0.3916-0.10140.1788-0.09230.00850.2087-0.16170.34820.05420.06770.4542-0.14120.350935.691116.947-36.9513
54.0911-0.35920.28145.44892.71861.40860.00960.0765-0.35250.05160.06110.31830.3316-0.2693-0.01450.295-0.05540.03690.23580.04960.37582.66148.5255-11.7444
61.3989-0.72030.23424.0122-0.65022.5847-0.24790.5550.0693-0.49260.6542-0.0013-0.33190.7215-0.31850.5259-0.1622-0.00880.9983-0.12140.320921.167620.8995-58.0693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 181)A1 - 181
2X-RAY DIFFRACTION2(chain 'B' and resid 2 through 192)B2 - 192
3X-RAY DIFFRACTION3(chain 'C' and resid 2 through 181)C2 - 181
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 193)D3 - 193
5X-RAY DIFFRACTION5(chain 'G' and resid 5 through 19)G5 - 19
6X-RAY DIFFRACTION6(chain 'H' and resid 1 through 19)H1 - 19

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more